The Destruction of HYDRA was a global offensive that pitted the United States of America, Advanced Threat Containment Unit, and S.H.I.E.L.D. against HYDRA. After HYDRA's existence was revealed, the War on HYDRA began, and S.H.I.E.L.D. fought to dismantle HYDRA. The United States Armed Forces seemingly destroyed HYDRA, although several high-ranking members survived and went underground.
When Gideon Malick orchestrated the return of Hive from Maveth back to Earth, he thought he would be generously rewarded once Hive conquers the world. Acting on his lifelong beliefs, Malick did everything he could to help Hive spread his power. However, Malick quickly lost influence within HYDRA and his own daughter was killed by Hive. Malick eventually realized his mistake; he had freed the devil instead of the HYDRA god he had worshiped. When S.H.I.E.L.D. captured Malick, he provided Phil Coulson with key information about HYDRA, to avenge Stephanie and help stop Hive.
Phil Coulson quickly passed Gideon Malick's intel to Glenn Talbot. Using the full power of the Advanced Threat Containment Unit and the United States Air Force, Talbot led a full-scale assault on all known HYDRA bases, with many HYDRA operatives killed or incarcerated. At least 17 bases and hideouts were captured, along with all the equipment at these bases.
After learning about Malick's betrayal, Fischer called Hale to his office, as they were one of the highest-ranking HYDRA moles within the US military. As he was trying to destroy incriminating documents Fischer informed Hale about HYDRA's success in reactivating the Chitauri tech obtained in the aftermath of the Battle of New York and establishing contact with an extraterrestrial intergalactic alliance called the Confederacy. Just as Fischer gave Hale the keys to his secret vault so she could take over his job and maintain HYDRA's contact with the aliens a small group of soldiers led by General Talbot burst into the room. Not knowing that Hale was HYDRA too Talbot asked her to step away from Fischer who took a cyanide pill and poisoned himself.
Hive, his Inhuman followers, and a remaining few HYDRA operatives successfully evaded Talbot's men and escaped the decimation of HYDRA, eventually creating a new base in Union City, an abandoned town in Wyoming which was bought by Hive with Gideon Malick's money. However, Hive was too focused on creating a better world for Inhumans and raising an Inhuman army to care about reforming HYDRA. Without a head that cared about rebuilding it, the majority of HYDRA was left in shambles.
Following an encounter with Talbot Hale came to the HYDRA Preparatory Academy which was abandoned by all but two, her own daughter Ruby, and one of the professors, Steger, who was trying to make Ruby complete her training by shooting her own pet dog. Ruby refused to comply, claiming that following the antiquated traditions had brought HYDRA to the brink of extinction. As a firm believer in HYDRA's authoritarian and survivalist ideology, Steger continued with his lecture, but Hale shot him dead, leaving Ruby and her mother as the last two heads of HYDRA.
In the offensive, the US forces dealt a crippling blow to HYDRA, as Matthew Ellis announced to the public that HYDRA was eradicated. Through a covert operation similar in nature to Operation Paperclip a former S.H.I.E.L.D. Academy student Tony Caine created new identities and new lives for those who were blackmailed into serving HYDRA, giving them a second chance.
However, several HYDRA leaders and operatives escaped justice. Three members of the HYDRA faction that worshiped Hive, led by Kirk Vogel, managed to evade the authorities, and assembled in Union City. They all died in Hive's unsuccessful attempt to turn them into Inhumans as a reward for their loyalty.
Another high ranking member of HYDRA, Vasily Karpov, the leader of the Winter Soldier Program, was captured, tortured, and killed by Helmut Zemo on a quest to avenge the deaths of his family by destroying the Avengers. Using Karpov's files, Zemo managed to gain access to the HYDRA Siberian Facility where he killed the five Winter Soldiers who were sleeping in suspended animation.
However, despite all those losses, some support for HYDRA's ideology remained, evidenced by the graffiti found in some American cities. Several former HYDRA operatives found employment as mercenaries working for another terrorist organization, the Watchdogs. Hale and her daughter Ruby also evaded capture and proceeded to build a new version of HYDRA based in the HYDRA Preparatory Academy. With Fischer's Phase Harmonic Teleportation Device Hale successfully established and maintained contact with the Confederacy.
However, her experience with the aliens and the news about the approaching intergalactic war convinced her to restart Project Destroyer of Worlds, a program started by Daniel Whitehall which was abandoned after Whitehall's death at the hands of Phil Coulson. Unlike Whitehall, who intended to make HYDRA's new leader, Hale hoped she could use the Particle Infusion Chamber to make a super soldier that would defend the Earth from all the threats from other worlds.
In chronological order:
- Agents of S.H.I.E.L.D.
- WHiH Newsfront
- Agents of S.H.I.E.L.D.
- WHIH Newsfront: The Avengers and The White House
- Agents of S.H.I.E.L.D. 3.17: The Team
- Agents of S.H.I.E.L.D. 3.18: The Singularity
- Agents of S.H.I.E.L.D.: 5.15: Rise and Shine
- Agents of S.H.I.E.L.D.: 5.13: Principia
- Agents of S.H.I.E.L.D.: 3.19: Failed Experiments
- Captain America: Civil War
- Twitter Profile/WHiH
- Agents of S.H.I.E.L.D.: 4.10: The Patriot